Support user-provided directory of `*.prompt.md` files

[data-douser]

Enable users to extend the MCP server with custom prompts by specifying an additional directory of *.prompt.md files at startup.

Configuration

Add new CLI/environment option:

--prompts-dir <path>    Additional directory of *.prompt.md files
CODEQL_MCP_PROMPTS_DIR  Environment variable alternative

Implementation Design

1. Extend server/src/prompts/prompt-loader.ts

   • Accept optional additionalPromptDirs: string[] parameter
   • Validate directory exists and is readable
   • Merge user prompts with built-in prompts (user prompts take precedence on conflict)

2. Prompt Discovery

   • Recursively scan directory for *.prompt.md files
   • Parse front-matter for prompt metadata (name, description, arguments)
   • Validate prompt schema matches MCP prompt specification

3. Server Startup Integration

   • Parse --prompts-dir in ql-mcp-server.ts
   • Load and register user prompts after built-in prompts
   • Log discovered user prompts at startup

Acceptance Criteria

• User prompts directory configurable via CLI and env var
• Conflicts handled with user prompts taking precedence
• Invalid prompt files logged as warnings (non-fatal)
• Unit tests for prompt discovery and merging logic